The Magpies coach had said that the Latics should open up extra seats to away fans as Newcastle's support could double the 4,500 they were assigned.
He urged fans to turn up to the DW Stadium in droves without tickets, prompting Wigan officials to declare that any Newcastle fans found in the home end will be ejected.
Pardew has now apologised over the remarks, which he claims were misinterpreted.
"I would like to apologise to anyone who may have misinterpreted the comments I made about our supporters travelling to Wigan on Saturday," he said.
"I have nothing but respect for Wigan Athletic as a club and clearly would never wish to interfere with any ticketing or safety issues Wigan have in place at their stadium.
"I was simply trying to encourage as many of our fans as possible to get to the game to cheer us on, but of course only through legitimate means."
Champions League-chasing Newcastle travel to Wigan on Saturday, with the home side sitting just one point above the drop zone.